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Coastal ecosystems worldwide are facing unprecedented challenges due to ever increasing human activities, resulting in increased land-derived stressors that can threaten the health and integrity of these systems. Mangrove forests are unique ecosystems that play a crucial role in filtering nutrients, retaining pollutants, and sequestering carbon. However, to what extent they are impacted by an intensification of human pressures is unclear and empirical evidence of landscape scale effects of a holistic view of the ecosystem is scarce. This thesis investigates the effects of human land use on several aspects of temperate mangrove ecosystems and aims to identify potential vulnerabilities of ecosystem processes to provide a holistic view on the impacts that humas are having on these important ecosystems. By working across a broad gradient of human land use, the first chapter establishes a connection between human land use intensity in catchments and regionally generalizable trends in mangrove forest structure and physicochemical parameters in sediments. Highlighting the integrated nature of anthropogenic impacts, this chapter emphasizes the need for holistic evaluations in assessing responses of complex natural systems to change. The second chapter investigates environmental controls on organic matter degradation in mangrove forests. Results from this study emphasize the importance of considering multiple factors influencing degradation processes, that vary with the quality of the decaying organic matter. Furthermore, using the human land use gradient from the previous chapter, this study identifies an impact of human land use through eutrophication on the rate of labile organic matter loss from mangrove sediments. The third chapter provides insights into bacterial communities in temperate mangrove sediments, revealing the persistent effects of nutrient enrichment even after the biochemical signal is lost. The study highlights the spatial resolution needed to detect impa

Estuaries and shallow lagoons are the most productive marine systems in the world and contribute to the maintenance of coastal biodiversity by providing various unique habitats for aquatic species. However, due to the inputs of nutrients, sediments and pollutants from the surrounding landscape, light availability and primary productivity can be strongly restricted, which may trigger rapid ecological change over time and cause substantial loss of coastal flora and fauna. This thesis explores the use of Sentinel-2 remote sensing imagery to monitor water properties of shallow intertidal tidal estuaries, for the purposes of managing the estuaries of New Zealand. The first goal (Chapter 2) was to develop a method to remove the influence of water bottom substrate reflectance in order to detect the true water colour (represented by dominant wavelength) and diffuse attenuation coefficients from Sentinel-2 imagery, in the case study estuary of Tauranga Harbour. The new methodology used direct measurement of bottom reflectance of intertidal areas while exposed, and used a regression estimator to derive subtidal bottom reflectance from particle size (developed using the intertidal properties). The method required the water depth to be known (from LiDAR) and reflectance observations from multiple water depths (either extracted along transects or at the same location at different tides). The method was applied to all available Sentinel-2 images and showed seasonal fluctuations and strong correlations with chlorophyll-a, suspended sediments and coloured metal ions collected by the regional council monitoring programme. This methodology was then applied to 12 estuaries and the results were interpreted in terms of ecological changes (Chapter 5). The second goal (Chapter 3) was to detect the distribution or density of seagrass/sandflats (where microphytobenthos (MPB) thrive) and use this as a basis to estimate their gross primary productivity (GPP). The new methodology combined Sent

Soft sediment benthic ecosystems are highly productive habitats which provide humans with a variety of valued resources and ecosystem services globally. However, coastal environments are subject to ongoing and increasing levels of anthropogenic stress which urgently needs to be quantified and strategically managed to balance socioeconomic resource interests. To support a more holistic approach to Marine Spatial Planning and better inform management decisions, spatial assessment approaches are needed which quantify the accumulating impact of multiple stressors on coastal species and habitats. This thesis investigates stressor-induced change in the density and distribution of subtidal benthic invertebrates from two globally pervasive stressors (sedimentation and bottom fishing), to develop spatial assessment tools useful to inform marine spatial management decisions. For many benthic species, their functional capacity is inherently density-dependent, and environmental stressors can impact population density, hence limiting the functional capacity of species and their ability to contribute to ecosystem processes and overall ecosystem health. A holistic approach to MSP needs to address the ways in which humans can cumulatively use, and also impact the environment, but it is difficult to measure the impact an environmental stressor can cause without first quantifying the current density and distribution of key species that they effect. Furthermore, it can often be challenging to obtain species records measuring abundance, density, or species richness within certain geographical locations, due to data scarcity, even if more data is available over a broader spatial scale. Probability of occurrence, abundance, and density was predicted using Species Distribution Models (SDMs) for seven functionally distinct benthic invertebrates, over two different spatial scales to compare the difference in model performance and usefulness of predictions made using data-rich national scale

Ecological functions in estuarine seagrass and unvegetated soft sediment habitats underpin many valuable ecosystem services. However, changing land-use and climate are accelerating inputs of fine terrestrial sediments, threatening these habitats. The prolonged suspension of fine sediments can reduce seafloor light availability and long-term accumulations increase sediment mud content (particles < 63 µm), both of which could have significant consequences on ecosystem functioning. Understanding how ecosystem functioning may respond to environmental change is vital to estuary management. In this thesis, I investigated the short- and long-term effects of elevated terrestrial sediment inputs on benthic primary production and nutrient cycling in intertidal seagrass meadows (Zostera muelleri) and microphytobenthos-dominated unvegetated habitats. To investigate the effects of reduced seafloor light availability and prolonged submergence periods resulting from global heating induced sea-level rise, I conducted a two-year seasonal in situ assessment of photosynthesis-irradiance relationships during submerged and emerged conditions in an adjacent seagrass meadow and unvegetated sandflat. Submerged gross primary production (GPP) in both habitats and emerged GPP in the seagrass habitat were strongly controlled by light availability. Higher rates of light-saturated GPP were found during submerged periods compared to emerged periods in both habitats, but this difference was most pronounced in the unvegetated habitat. If the water-column remains clear, sea-level rise could therefore increase daily GPP in soft sediment habitats. However, declines in submerged GPP with increased water-column turbidity will be exacerbated with sea-level rise. Across a natural mud content gradient, I measured primary production in seagrass and unvegetated habitats to address the long-term implications of elevated sediment inputs. In sediments with ≤ 35 % mud content, net primary production (NPP) and GP